scholarly journals Bacterial gastroenteritis caused by the putative zoonotic pathogen Campylobacter lanienae: First reported case in Germany

2021 ◽  
Author(s):  
Juliane Fornefett ◽  
Anne Busch ◽  
Sandra Döpping ◽  
Helmut Hotzel ◽  
Dagmar Rimek
Keyword(s):  
Type Species ◽  
Campylobacter Coli ◽  
Pathogenic Potential ◽  
Content Type ◽  
Link Type ◽  
First Case ◽  
Strain Collection ◽  
Causative Agents ◽  
Bacterial Gastroenteritis ◽  
Abattoir Workers

Foodborne campylobacteriosis is the most common cause of human bacterial enteritis in Germany. Campylobacter jejuni and Campylobacter coli are the main causative agents for enteric disease, but a number of other species are involved, including rare ones. These rare Campylobacter spp. are emerging zoonotic pathogens in humans due to increasing international movement of supplies, livestock and people. Campylobacter lanienae was first isolated from healthy abattoir workers in Switzerland and at first its pathogenic potential for humans was considered to be low. Recently, the first case of Campylobacter lanienae -associated human enteritis was reported in Canada. Here, we describe a case of mild Campylobacter lanienae -associated enteritis with subsequent asymptomatic excretion in a butcher. The isolate is available at the TLV strain collection (no. TP00333/18). This first reported case of human Campylobacter lanienae campylobacteriosis in Germany demonstrates the agent’s likely zoonotic pathogenicity.

scholarly journals Sneathia amnii bacteraemia and chorioamnionitis leading to second trimester abortion: a case report

2021 ◽  
Vol 3 (12) ◽  
Author(s):  
Lien Gruwier ◽  
Aaron Sprenkels ◽  
Sofie Hulsbosch ◽  
Anne Vankeerberghen ◽  
Reinoud Cartuyvels
Keyword(s):  
Type Species ◽  
Culture Broth ◽  
Second Trimester ◽  
Trimester Abortion ◽  
Content Type ◽  
Link Type ◽  
First Case ◽  
Gene Sequence Analysis ◽  
The Usa ◽  
Septic Abortion

Background. Sneathia amnii (formerly designated as Leptotrichia amnionii ) was first described in 2002 in the USA. Members of the genus Sneathia can be part of the normal flora of the genitourinary tract, but have been implicated in invasive (mostly gynaecological) infections. Case presentation. To the best of our knowledge, here we present the first case of S. amnii infection in Belgium, in a young woman presenting with fever leading to second trimester septic abortion. Conclusions. Despite its pathogenicity, S. amnii remains an underrated cause of infections due to inherent difficulties with conventional laboratory methods. By extracting the bacterial DNA directly from the blood culture broth and performing a 16S ribosomal RNA gene sequence analysis we succeeded in identifying S. amnii as the most probable cause of the septic abortion in our patient.

scholarly journals First case report of post-operative infection due to Francisella tularensis after cardiac surgery

2019 ◽  
Vol 1 (8) ◽  
Author(s):  
Arif Maqsood Ali ◽  
Muhammad Noor ul Amin ◽  
Shazia Arif
Keyword(s):  
Cardiac Surgery ◽  
Case Report ◽  
Francisella Tularensis ◽  
Type Species ◽  
Detection Methods ◽  
Culture Bottle ◽  
Content Type ◽  
Chest Infection ◽  
Link Type ◽  
First Case

Background. Francisella tularensis is a rare zoonotic bacterium that spreads sporadically by various routes, including infected arthropod bites, ingestion of contaminated water and inhalation of contaminated dust. However, its occurrence in postoperative chest infection has never been reported. Pathogen isolation, serology and molecular detection methods are commonly used for the diagnosis of tularaemia. Case presentation. We present the first case report of the isolation of F. tularensis from a patient with a chest infection (a boy in his teens) following cardiac surgery for closure of a ventral septal defect. It was isolated on blood and chocolate agar on the third day after the subculture of drain fluid collected in a blood culture bottle incubated in Bact T/Alert 3-D (bioMerieux, France). The organism was identified as F. tularensis by Vitek GN ID Cards (Vitek 2 Compact, bioMerieux, France). The patient made a smooth recovery with antibiotic therapy. Conclusion. F. tularensis can cause post-operative infection, especially in patients with a rural background.

scholarly journals Molecular epidemiology and phylogenomic analysis of Mycobacterium abscessus clinical isolates in an Asian population

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Ka Lip Chew ◽  
Sophie Octavia ◽  
Roland Jureen ◽  
Oon Tek Ng ◽  
Kalisvar Marimuthu ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Type Species ◽  
Asian Population ◽  
Bioinformatic Analysis ◽  
Mycobacterium Abscessus ◽  
Phylogenomic Analysis ◽  
Pathogenic Potential ◽  
Content Type ◽  
Link Type ◽  
Sequence Types

Mycobacterium abscessus comprises three subspecies: M. abscessus subsp. abscessus , M. abscessus subsp. bolletii , and M. abscessus subsp. massiliense . These closely related strains are typically multi-drug-resistant and can cause difficult-to-treat infections. Dominant clusters of isolates with increased pathogenic potential have been demonstrated in pulmonary infections in the global cystic fibrosis (CF) population. An investigation was performed on isolates cultured from an Asian, predominantly non-CF population to explore the phylogenomic relationships within our population and compare it to global M. abscessus isolates. Whole-genome-sequencing was performed on M. abscessus isolates between 2017 and 2019. Bioinformatic analysis was performed to determine multi-locus-sequence-type, to establish the phylogenetic relationships between isolates, and to identify virulence and resistance determinants in these isolates. A total of 210 isolates were included, of which 68.5 % (144/210) were respiratory samples. These isolates consisted of 140 (66.6 %) M . abscessus subsp. massiliense , 67 (31.9 %) M . abscessus subsp. abscessus, and three (1.4 %) M . abscessus subsp. bolletii . Dominant sequence-types in our population were similar to those of global CF isolates, but SNP differences in our population were comparatively wider despite the isolates being from the same geographical region. ESX (ESAT-6 secretory) cluster three appeared to occur most commonly in ST4 and ST6 M. abscessus subsp. massiliense , but other virulence factors did not demonstrate an association with isolate subspecies or sample source. We demonstrate that although similar predominant sequence-types are seen in our patient population, cross-transmission is absent. The risk of patient-to-patient transmission appears to be largely limited to the vulnerable CF population, indicating infection from environmental sources remains more common than human-to-human transmission. Resistance and virulence factors are largely consistent across the subspecies with the exception of clarithromycin susceptibility and ESX-3.

scholarly journals Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Lin Zhao ◽  
Hongyou Chen ◽  
Xavier Didelot ◽  
Zhenpeng Li ◽  
Yinghui Li ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Vibrio Parahaemolyticus ◽  
Type Species ◽  
Genomic Islands ◽  
Content Type ◽  
Pan Genome ◽  
Link Type ◽  
Gene Segregation ◽  
Strain Collection ◽  
The Usa

Vibrio parahaemolyticus is an important cause of foodborne gastroenteritis globally. Thermostable direct haemolysin (TDH) and the TDH-related haemolysin are the two key virulence factors in V. parahaemolyticus. Vibrio pathogenicity islands harbour the genes encoding these two haemolysins. The serotyping of V. parahaemolyticus is based on the combination of O and K antigens. Frequent recombination has been observed in V. parahaemolyticus , including in the genomic regions encoding the O and K antigens. V. parahaemolyticus serotype O4:K12 has caused gastroenteritis outbreaks in the USA and Spain. Recently, outbreaks caused by this serotype of V. parahaemolyticus have been reported in China. However, the relationships among this serotype of V. parahaemolyticus strains isolated in different regions have not been addressed. Here, we investigated the genome variation of the V. parahaemolyticus serotype O4:K12 using the whole-genome sequences of 29 isolates. We determined five distinct lineages in this strain collection. We observed frequent recombination among different lineages. In contrast, little recombination was observed within each individual lineage. We showed that the lineage of this serotype of V. parahaemolyticus isolated in America was different from those isolated in Asia and identified genes that exclusively existed in the strains isolated in America. Pan-genome analysis showed that strain-specific and cluster-specific genes were mostly located in the genomic islands. Pan-genome analysis also showed that the vast majority of the accessory genes in the O4:K12 serotype of V. parahaemolyticus were acquired from within the genus Vibrio . Hence, we have shown that multiple distinct lineages exist in V. parahaemolyticus serotype O4:K12 and have provided more evidence about the gene segregation found in V. parahaemolyticus isolated in different continents.

scholarly journals Streptococcus lutetiensis neonatal meningitis with empyema

2021 ◽  
Vol 3 (9) ◽  
Author(s):  
Allen T. Yu ◽  
Kate Shapiro ◽  
Christy A. Beneri ◽  
Lisa S. Wilks-Gallo
Keyword(s):  
United States ◽  
Neonatal Sepsis ◽  
Type Species ◽  
The United States ◽  
Neonatal Meningitis ◽  
Content Type ◽  
Link Type ◽  
First Case

Streptococcus lutetiensis has been known to cause sepsis in adults, but only one case regarding neonatal sepsis has been reported internationally, with no sequelae. We report the first case of neonatal bacteremia and meningitis with empyema caused by S. lutetiensis in the United States.

scholarly journals Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates

2020 ◽  
Author(s):  
Jo Hendrix ◽  
L. Elaine Epperson ◽  
David Durbin ◽  
Jennifer R. Honda ◽  
Michael Strong
Keyword(s):  
Type Species ◽  
Mycobacterium Abscessus ◽  
Genomic Variation ◽  
Diagnostic Methods ◽  
Pathogenic Potential ◽  
Circular Chromosome ◽  
Content Type ◽  
Link Type ◽  
Complete Genomes ◽  
Long Read

Mycobacterium kubicae is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft tissue infections. Although numerous studies have investigated the genetic variation among prevalent clinical NTM species, including Mycobacterium abscessus and Mycobacterium avium , many of the less common but clinically relevant NTM species, including M. kubicae , still lack complete genomes to serve as a comparative reference. Well-characterized representative genomes for each NTM species are important both for investigating the pathogenic potential of NTM, as well as for use in diagnostic methods, even for species that less frequently cause human disease. Here, we report the complete genomes of two M. kubicae strains, isolated from two unrelated patients. Hybrid short-read and long-read sequencing and assembly, using sequence reads from Illumina and Oxford Nanopore Technologies platforms, were utilized to resolve the chromosome and plasmid sequences of each isolate. The genome of NJH_MKUB1 had 5135 coding sequences (CDSs), a circular chromosome of length 5.3 Mb and two plasmids. The genome of NJH_MKUB2 had 5957 CDSs, a circular chromosome of 6.0 Mb and five plasmids. We compared our completed genomic assemblies to four recently released draft genomes of M. kubicae in order to better understand intraspecies genomic conservation and variability. We also identified genes implicated in drug resistance, virulence and persistence in the M. kubicae chromosome and plasmids. Virulence factors encoded in the genome and in the plasmids of M. kubicae provide a foundation for investigating how opportunistic environmental NTM may cause disease.

scholarly journals Mycobacterium mucogenicum meningitis due to external ventricular drain

2020 ◽  
Vol 2 (11) ◽  
Author(s):  
Salwa Moiz ◽  
Omar Rahman ◽  
Mark Morcos ◽  
Asma Siddiqui ◽  
Usman Bin Hameed
Keyword(s):  
Type Species ◽  
Obstructive Hydrocephalus ◽  
External Ventricular Drain ◽  
Response To Therapy ◽  
Case Presentation ◽  
Content Type ◽  
Link Type ◽  
First Case ◽  
Neurological Exam ◽  
Mycobacterium Mucogenicum

Introduction. Mycobacterium mucogenicum is a rare non-tuberculous organism associated with catheter-related infections when pathogenic in humans. We present the first case of an external ventricular drain (EVD)-associated M. mucogenicum meningitis. Case presentation. A 55-year-old woman had EVD placement for obstructive hydrocephalus following traumatic subarachnoid haemorrhage. Cerebrospinal fluid (CSF) was obtained 5 days later for fever and neurological changes. M. mucogenicum was ultimately isolated from the CSF and the patient was placed on appropriate antibiotics. Her management included replacement of the EVD and a prolonged course of anti-mycobacterial antibiotics. CSF findings showed her response to therapy and neurological exam improved after 6 weeks. Conclusion. M. mucogenicum infections are very rare and existing reports indicate that it may be a device- or catheter-related pathogen. This microorganism has not been previously associated with an EVD. Ours may be the first documented report of EVD-related M. mucogenicum infection.

Flavobacterium tagetis sp. nov., a novel urea-hydrolysing bacterium isolated from the roots of Tagetes patula

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Geeta Chhetri ◽  
Inhyup Kim ◽  
Minchung Kang ◽  
Jiyoun Kim ◽  
Yoonseop So ◽  
...  
Keyword(s):  
Type Species ◽  
Close Relative ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
Tagetes Patula ◽  
Biochemical Tests ◽  
Pathogenic Potential ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, rod-shaped, motile by gliding, non-sporulating and strictly aerobic bacterium, designated strain GN10T, was isolated from the roots of Tagetes patula, collected from the garden of Dongguk University, Goyang, Republic of Korea. The cells could grow at 10–42 °C and at pH 5.5–9.0. Strain GN10T was sensitive to NaCl and tolerated up to 4 % NaCl (w/v). Comparative analysis of 16S rRNA gene sequences revealed the highest similarities to Flavobacterium tistrianum GB 56.1T (98.9 %), Flavobacterium sharifuzzamanii A7.6T (98.6 %), Flavobacterium zhairuonense A5.7T (98.3 %) and Flavobacterium anhuiense D3T (98 %). Phylogenetic analysis showed that strain GN10T clustered within the genus Flavobacterium and formed a monophyletic cluster with its close relative members. The average nucleotide identity and digital DNA–DNA hybridization values between strain GN10T and related species belonging to the genus Flavobacterium were well below the standard threshold for prokaryotic species delineation. The DNA G+C content of strain GN10T was 33.6 mol%. The predominant cellular fatty acids (>10 %) were identified as iso-C15 : 0, C16 : 0 and summed feature 3 (C16  : 1 ω6c and/or C16  :  1 ω7c). Strain GN10T contained menaquinone 6 as the major respiratory quinone. The major polar lipids were phosphatidylethanolamine, three unidentified aminoglycolipids, two unidentified glycolipids, one unidentified phosphoglycolipid and five unidentified lipids. Urease is a nickel-containing enzyme found in archaea, bacteria, plants and unicellular eukaryotes. It serves as a virulence factor and is responsible for pathogenesis in humans and animals. Here, we describe a novel urease-hydrolysing bacterium, strain GN10T. The urease activity of this strain may serve as an indicator of pathogenic potential and drug resistance, which may facilitate the development of many diseases. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain GN10T from its closely related members and considered to represent novel species in the genus Flavobacterium , for which the name Flavobacterium tagetis (GN10T=KCTC 82695T=NBRC 114841T) is proposed.

scholarly journals A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Arnoud H. M. van Vliet ◽  
Oliver J. Charity ◽  
Mark Reuter
Keyword(s):  
Type Species ◽  
Campylobacter Coli ◽  
Bacterial Populations ◽  
Content Type ◽  
Microbial Genomes ◽  
Link Type ◽  
Cas9 Protein ◽  
History Of ◽  
Integrative Conjugative Elements ◽  
Integrative And Conjugative Element

Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICEs) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanisms such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution of the pVir, pTet and PCC42 plasmids and a new 70–129 kb ICE (CampyICE1) in the foodborne bacterial pathogens Campylobacter jejuni and Campylobacter coli . CampyICE1 contains a degenerated Type II-C CRISPR system consisting of a sole Cas9 protein, which is distinct from the previously described Cas9 proteins from C. jejuni and C. coli . CampyICE1 is conserved in structure and gene order, containing blocks of genes predicted to be involved in recombination, regulation and conjugation. CampyICE1 was detected in 134/5829 (2.3 %) C . jejuni genomes and 92/1347 (6.8 %) C . coli genomes. Similar ICEs were detected in a number of non-jejuni/coli Campylobacter species, although these lacked a CRISPR-Cas system. CampyICE1 carries three separate short CRISPR spacer arrays containing a combination of 108 unique spacers and 16 spacer-variant families. A total of 69 spacers and 10 spacer-variant families (63.7 %) were predicted to target Campylobacter plasmids. The presence of a functional CampyICE1 Cas9 protein and matching anti-plasmid spacers was associated with the absence of the pVir, pTet and pCC42 plasmids (188/214 genomes, 87.9 %), suggesting that the CampyICE1-encoded CRISPR-Cas has contributed to the exclusion of competing plasmids. In conclusion, the characteristics of the CRISPR-Cas9 system on CampyICE1 suggests a history of plasmid warfare in Campylobacter .

scholarly journals Campylobacter novaezeelandiae sp. nov., isolated from birds and water in New Zealand

2020 ◽  
Vol 70 (6) ◽  
pp. 3775-3784 ◽  
Author(s):  
Samuel Bloomfield ◽  
David Wilkinson ◽  
Lynn Rogers ◽  
Patrick Biggs ◽  
Nigel French ◽  
...  
Keyword(s):  
New Zealand ◽  
Type Species ◽  
Genetic Relationships ◽  
Rrna Gene ◽  
Campylobacter Coli ◽  
Biochemical Tests ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Link Type ◽  
Maldi Tof

Six isolates of Campylobacter with similar non-standard colonial morphologies were identified during studies isolating Campylobacter from bird faeces and rivers in New Zealand. Genomic (16S rRNA gene sequencing and whole genome analysis) and phenotypic (MALDI-TOF analysis and conventional biochemical tests) showed that the isolates form a monophyletic clade with genetic relationships to Campylobacter coli / Campylobacter jejuni and Campylobacter peloridis /Campylobacter amoricus. They may be distinguished from other Campylobacter by their MALDI-TOF spectral pattern, their florid α-haemolysis, their ability to grow anaerobically at 37 °C, and on 2 % NaCl nutrient agar, and their lack of hippuricase. This study shows that these isolates represent a novel species within the genus Campylobacter for which the name Campylobacter novaezeelandiae sp. nov. is proposed. The presence of C. novaezeelandiae in water may be a confounder for freshwater microbial risk assessment as they may not be pathogenic for humans. The type strain is B423bT (=NZRM 4741T=ATCC TSD-167T).

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